2NDSCORE(1)						  User Contributed Documentation					       2NDSCORE(1)

NAME

	 2ndscore  - find the best hairpin anchored at each position.

SYNOPSIS

	2ndscore in.fasta > out.hairpins

DESCRIPTION

       For every position in the sequence this will output a line:

	  -0.6	52 ..  62      TTCCTAAAGGTTCCA	GCG CAAAA TGC  CATAAGCACCACATT
	(score) (start .. end) (left context)	(hairpin)      (right contenxt)

       For positions near the ends of the sequences, the context may be padded with 'x' characters. If no hairpin can be found, the score will be
       'None'.

       Multiple fasta files can be given and multiple sequences can be in each fasta file. The output for each sequence will be separated by a
       line starting with '>' and containing the FASTA description of the sequence.

       Because the hairpin scores of the plus-strand and minus-strand may differ (due to GU binding in RNA), by default 2ndscore outputs two sets
       of hairpins for every sequence: the FORWARD hairpins and the REVERSE hairpins. All the forward hairpins are output first, and are
       identified by having the word 'FORWARD' at the end of the '>' line preceding them. Similarly, the REVERSE hairpins are listed after a '>'
       line ending with 'REVERSE'. If you want to search only one or the other strand, you can use:

	   --no-fwd    Don't print the FORWARD hairpins
	   --no-rvs    Don't print the REVERSE hairpins

       You can set the energy function used, just as with transterm with the --gc, --au, --gu, --mm, --gap options. The --min-loop, --max-loop,
       and --max-len options are also supported.

   FORMAT OF THE .BAG FILES
       The columns for the .bag files are, in order:

	       1. gene_name
	       2. terminator_start
	       3. terminator_end
	       4. hairpin_score
	       5. tail_score
	       6. terminator_sequence

	   7. terminator_confidence: a combination of the hairpin and tail score that
	      takes into account how likely such scores are in a random sequence. This
	      is the main "score" for the terminator and is computed as described in
	      the paper.

	   8. APPROXIMATE_distance_from_end_of_gene: The *approximate* number of base
	      pairs between the end of the gene and the start of the terminator. This
	      is approximate in several ways: First, (and most important) TransTermHP
	      doesn't always use the real gene ends. Depending on the options you give
	      it may trim some off the ends of genes to handle terminators that
	      partially overlap with genes. Second, where the terminator "begins"
	      isn't that well defined.	This field is intended only for a sanity check
	      (terminators reported to be the best near the ends of genes shouldn't be
	      _too far_ from the end of the gene).

   USING TRANSTERM WITHOUT GENOME ANNOTATIONS
       TransTermHP uses known gene information for only 3 things: (1) tagging the putative terminators as either "inside genes" or "intergenic,"
       (2) choosing the background GC-content percentage to compute the scores, because genes often have different GC content than the intergenic
       regions, and (3) producing slightly more readable output. Items (1) and (3) are not really necessary, and (2) has no effect if your genes
       have about the same GC-content as your intergenic regions.

       Unfortunately, TransTermHP doesn't yet have a simple option to run without an annotation file (either .ptt or .coords), and requires at
       least 2 genes to be present. The solution is to create fake, small genes that flank each chromosome. To do this, make a fake.coords file
       that contains only these two lines:

	       fakegene1       1 2     chome_id
	       fakegene2       L-1 L   chrom_id

       where L is the length of the input sequence and L-1 is 1 less than the length of the input sequence. "chrom_id" should be the word directly
       following the ">" in the .fasta file containing your sequence. (If, for example, your .fasta file began with ">seq1", then chrom_id =
       seq1).

       This creates a "fake" annotation with two 1-base-long genes flanking the sequence in a tail-to-tail arrangement: --> <--. TransTermHP can
       then be run with:

	       transterm -p expterm.dat sequence.fasta fake.coords

       If the G/C content of your intergenic regions is about the same as your genes, then this won't have too much of an effect on the scores
       terminators receive.  On the other hand, this use of TransTermHP hasn't been tested much at all, so it's hard to vouch for its accuracy.

SEE ALSO

       transterm(1)

AUTHOR

       Alex Mestiashvili <alex@biotec.tu-dresden.de>

								    2011-02-19							       2NDSCORE(1)